Your Flowdock desktop version under Windows 10 is considered a 'Windows App'. Windows 10 allows you to enable or disable the notifications of your apps. It will also allow you to control the active hours for these notifications.
First, you need to have the "Enable Notifications From Apps and other senders" set:
Step 1: Click the Action Center icon located on the right-hand side of the Windows taskbar.
Step 2: Then, click the All Settings button with the gear icon.
Step 3: Select System in the top-left corner of the window.
Step 4: In “System,” click “Notifications & Actions” from the left-hand menu. This will take you to a screen providing access to all of the settings related to notifications and the Action Center.
Step 5: Turn on the "Get notifications from apps and other senders."
Then, you need to make certain you specify your Quiet Hours as you need them. Quiet Hours will suppress and prevent the notifications. You need to make certain to use the accurate Quiet Hours (if you need them).
If you hit Windows + A it will bring up the Action Center. Click Expand near the bottom to bring up more options, then hit "Quiet Hours". If you have it defined and don't need it, you can unset it.